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Figure 3 | BMC Biology

Figure 3

From: An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters

Figure 3

Error in the published Oenothera elata ycf2. (A) Alignment of ycf2 nucleotide sequences: The top two sequences, Oenothera biennis and O. elata, were sequenced as part of this study. We did not sequence the first ~1600 bp. The bottom two sequences correspond to the published Oenothera elata and Nicotiana tabacum sequences. The bottom three sequences were used to determine a consensus base at each position, and positions that did not match this consensus are colored as denoted in the key. (B) All codon position ML tree using the TVM+G model in PAUP* with 100 bootstrap replicates. Only the 3' region of ycf2 starting at position 4023 of the published Oenothera sequence [31] was obtained for the four Myrtales taxa (Eucalyptus, Fuchsia, Clarkia and Epilobium) and the analysis was performed using this region of aligned positions as indicated in (A). Within this region, gappy positions were removed prior to phylogenetic analysis, which resulted in 2567 positions. When the entire gene was used with the published Oenothera sequence excluded, the topology was the same except that the Lotus and Arabidopsis branches were switched. When the published Oenothera is included in the full-length analysis, its strong chimerism pulled Clarkia, Epilobium and our elata sequence into an artifactual clade with the published elata gene at the base of the Solanaceae.

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